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Gene-level analysis #40

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merged 11 commits into from
Jun 1, 2022
Merged

Gene-level analysis #40

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95e0cb4
Add gene level analysis
filosi May 25, 2022
54dd563
Added test files for gene set
filosi May 31, 2022
cfc26ef
Upgrade pipeline for gene-level
filosi May 31, 2022
a3b9b00
Include instruction for testing gene-level analysis
filosi May 31, 2022
a0d9067
Change conf test
filosi May 31, 2022
ff2010c
Remove duplicate code
filosi May 31, 2022
3ffd440
Tweak base process for unified pipelin
filosi May 31, 2022
d57e2f4
Unify shared part of the pipeline
filosi May 31, 2022
8df089c
Add required parameters for gene level analysis
filosi May 31, 2022
86b69f4
Merge branch 'feature/gene_level_integration' into develop
filosi May 31, 2022
8aa287f
Update code for gene-level test
filosi May 31, 2022
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Tweak base process for unified pipelin
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@filosi
filosi committed May 31, 2022
commit 3ffd44074355caef1e4ebdbb696087d9b4f46b5c
1 change: 1 addition & 0 deletions conf/test_gene.config
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Expand Up @@ -22,6 +22,7 @@ params {
regenie_test = 'additive'
annotation_min_log10p = 2
regenie_bsize_step1 = 200
regenie_run_gene_tests = true
regenie_gene_masks = "$baseDir/tests/input/gene_level/example.masks"
regenie_gene_setlist = "$baseDir/tests/input/gene_level/example.setlist"
regenie_gene_annot = "$baseDir/tests/input/gene_level/example.annotation"
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4 changes: 2 additions & 2 deletions modules/local/regenie_gene_level.nf
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Expand Up @@ -12,8 +12,8 @@ process REGENIE_GENE {
path covariates_file

output:
tuple val(genotyped_plink_filename), path("*regenie.gz"), emit: regenie_gene_level_out
path "${genotyped_plink_filename}.log", emit: regenie_gene_level_out_log
tuple val(genotyped_plink_filename), path("*regenie.gz"), emit: regenie_step2_out
path "${genotyped_plink_filename}.log", emit: regenie_step2_out_log

script:
def firthApprox = params.regenie_firth_approx ? "--approx" : ""
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